The first published marker-assisted EPD has appeared in the American Simmental Association’s fall 2004 sire summary. “It’s a milestone for EPDs,” says Jim Gibb, senior manager of beef segment development for Merial’s IGENITY DNA business. “Since EPDs were first created, about 25 years ago, EPDs have come a long way. This is just the next step.”
So what does that mean for producers? Probably several things, but before we get to them, a couple of definitions in the genetic lexicon should probably be dispensed with first.
“Genome” refers to the set of genes an organism possesses. It is, in a sense, the blueprint of an animal. “Phenotype” refers to the organism’s actual physical properties: hair color, height, weight, etc. An organism’s genome has a large influence on its phenotype, but it is not the only factor; environment plays a big part, too. In fact, for most traits—those for which heritability is less than 50 percent—environment accounts for more variation than genotype.
Traditional EPDs are derived from the observable performance, or phenotype, of an individual and its relatives. They have been used to increase the frequency of favorable forms of many genes influencing a particular trait without any need to know which genes are involved.
DNA-based selection comes at the issue from the other side, by identifying the genes responsible for a given trait. Of course, it complicates matters that many traits are influenced by a number of genes, and there is no trait for which all relevant genes have been identified. That’s why experts say that current DNA tests won’t account for a lot of the variation out there.
Which brings us to markers. Even where the relevant genes may not have been identified, there may be markers that have been identified: they reside very close to the relevant gene and have a great chance of being inherited along with the desired gene. Marker-assisted EPDs, then, represent the merger of genotypes and phenotypes to enhance the calculations of EPDs.
“By melding genotypes into traditional genetic evaluation, we have provided the most rational means of presenting DNA data to the industry,” says Wade Shafer, director of performance programs for the ASA. “Until now, one of the challenges with DNA testing has been that the results are difficult, if not impossible, to correctly incorporate into a breeding program. The marker-assisted EPD assimilates phenotypes and marker results and presents the information in a usable form—the EPD,” Dr. Shafer says.
But how should it be interpreted—does a marker-assisted EPD mean more than a traditional EPD? “It depends on how accurate the regular EPD is,” says Mark Thallman, research geneticist at the Meat Animal Research Center. “If it’s an EPD on a bull with a high accuracy, then adding marker information should not change the evaluation greatly. But if you have a set of young bulls that are candidates to be the next generation of herd sires, and you have no phenotypic information on their carcass traits, marker information could add a lot, because we didn’t have a lot to start with.”
The value of a marker-assisted EPD also depends to some degree on the trait in question; if the heritability of the trait is high and it can be measured prior to the time at which selection decisions need to be made, the advantages of marker-assisted selection relative to selection with traditional EPDs is minimal, because the traditional EPDs estimate the breeding value of all the “unmarked” genes that contribute to a given trait.
Marker-assisted EPDs will also be helpful for those traits that are expensive to measure, and tenderness is a prime example of that category. “Incorporating DNA testing allows us to obtain those genotypes at an earlier age,” Dr. Gibb says. “We don’t have to get as much progeny data.”
Getting the data
There is much discussion about how the genetic information will be gathered and who will pay for its collection. This first instance may be a unique situation. “The American Simmental Association paid to have all the bulls in this genetic evaluation (which already had phenotypic data collected on their offspring through NCBA Carcass Merit program) genotyped by Frontier Beef Systems (recently acquired by Merial),” Dr. Shafer says. “Then, working with funds from the National Beef Cattle Evaluation Consortium, Dr. Richard Quaas of Cornell University developed the methodology to calculate marker-assisted EPDs. How the development of marker-assisted EPDs will be underwritten in the future is yet to be seen, though I think it’s a safe bet that breeders will directly shoulder more of the financial burden than they did in this effort. As with collecting phenotypic data, the responsibility and cost of collecting genotypic data will fall largely on the breeder.”
That means, to make it worth their while, the value derived from the genetic progress must outweigh expenses of collecting the marker information. Does it—or will it? “That’s a question very much up in the air,” says Dr. Shafer. “The answer depends on several variables, not the least of which is the cost of DNA testing. Because most quantitative traits are affected by many genes, it is unlikely that any one gene will have a major impact on a trait; therefore, to get much resolution we will need to have information on several markers that affect a trait.”
Right now, a test looks at one marker or a maybe couple of them, and the cost is substantial. If each new marker that comes along is priced similarly, the cumulative cost could be greater than the potential gain—particularly on traits that don’t have a major economic impact or where phenotypic data is easily collected. But that cost is likely to decrease as technology improves and competition increases.
“Of course, we may find genes that have a huge impact on a major trait,” Dr. Shafer says. “In such a case, the cost of the test will pale in comparison to the obvious benefit of knowing whether or not an animal carries the gene. At this point, however, we haven’t found those silver-bullet kind of genes.”
The cost of the testing can be compared to that of ultrasound or new EPDs: it’s an additional cost a producer may bear that in the long term, should add value to the product. “As producers do more testing, more genotypes will flow back to the associations, so associations can include it in their database,” Dr. Gibb says. And the best way for testing to provide a return on the investment is for the information to be incorporated into an EPD, where it can be easily used.
But Dr. Shafer offers a warning: “Until a marker is validated—in other words, it has been determined, through scientific scrutiny, to influence a trait—you should tread cautiously to avoid wasting your money by testing for it.” The NBCEC is setting up a process for evaluating genetic tests. “As we’ve set up the system, a lot of breeders and breed associations are interested in those results—which tests they should invest in,” Dr. Thallman says.
A commercial producer may use marker-assisted EPDs the same way as a traditional EPD: to screen bulls. “It won’t be that much different than how they currently use EPDs,” Dr. Gibb says. “That’s the beauty of it; they won’t look much different than they do today.”
One small change will be that the addition of the markers will mean more spread between the EPDs of high and low sires. “As you add more information, you get more spread,” Dr. Gibb says. “That’s because the values become more accurate.”
From a seedstock per-spective, the increased information in genetic evaluations incorporating DNA tests may provide opportunities to do some new things with mating systems, in addition to selection,” Dr. Thallman says.
In the future, the focus will be not just on output traits, but is expected to turn to traits that reduce input costs, with disease resistance and reproduction being areas of great promise for genotypic information, Dr. Gibb says. Such areas that are difficult or expensive to measure, like disease resistance, have low heritability or can only be measured late in life are where marker-assisted EPDs are likely to make their greatest impact.
Eventually, they will probably take the place of traditional EPDs, though that is several years away. A lot of things will need to happen: first, the collection and reporting of data, preferably directly from the lab to the breed association, Dr. Thallman says, because “it causes problems if breeders only turn in test results that they like. An all-or-nothing reporting policy would help, but we don’t currently have an infrastructure for that. Marker-assisted EPDs are expected to be part of a planned overhaul of the whole EPD system by the NBCEC, but that’s still five to 10 years out.”
Still, the time to start thinking about these new technologies may be now; Dr. Thallman believes early adopters will be in the best position to reap their benefits, partly because it takes so long to make genetic changes in cattle. “If you think there will be technology allowing cattle to be sold at different prices depending on their merit for tenderness 10 years from now, then the time to start making genetic changes is now,” Dr. Thallman says.